Reduce bioformats keeping file handles open

When bioformats tries to open a zip file, it opens the file once per
internal file.  If it fails to find a file that can be opened within the
zip, it throws an error and leaves all of the file handles open.  By
dividing the reader into more steps, we can ask to open an empty file,
which somehow releases the file handles.

CHANGELOG.md

@@ -10,6 +10,7 @@
 - Add a dependency to the zarr source to read more compression types ([#1480](../../pull/1480))
 - Guard fetching internal metadata on zarr sources that have less data ([#1481](../../pull/1481))
 - Add a method to list registered extensions and mimetypes ([#1488](../../pull/1488))
+- Reduce bioformats keeping file handles open ([#1492](../../pull/1492))
 
 ### Changes
 - Prohibit bioformats from reading zip directly ([#1491](../../pull/1491))

sources/bioformats/large_image_source_bioformats/__init__.py

@@ -221,7 +221,21 @@ def __init__(self, path, **kwargs):  # noqa
         try:
             javabridge.attach()
             try:
-                self._bioimage = bioformats.ImageReader(largeImagePath)
+                self._bioimage = bioformats.ImageReader(largeImagePath, perform_init=False)
+                try:
+                    # So this as a separate step so, if it fails, we can ask to
+                    # open something that does not exist and bioformats will
+                    # release some file handles.
+                    self._bioimage.init_reader()
+                except Exception as exc:
+                    try:
+                        # Ask to open a file that should never exist
+                        self._bioimage.rdr.setId('__\0__')
+                    except Exception:
+                        pass
+                    self._bioimage.close()
+                    self._bioimage = None
+                    raise exc
             except (AttributeError, OSError) as exc:
                 if not os.path.isfile(largeImagePath):
                     raise TileSourceFileNotFoundError(largeImagePath) from None